chr10-33180346-T-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_003873.7(NRP1):c.2502A>T(p.Glu834Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000414 in 1,449,360 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E834K) has been classified as Likely benign.
Frequency
Consequence
NM_003873.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NRP1 | NM_003873.7 | c.2502A>T | p.Glu834Asp | missense_variant | 17/17 | ENST00000374867.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NRP1 | ENST00000374867.7 | c.2502A>T | p.Glu834Asp | missense_variant | 17/17 | 1 | NM_003873.7 | P3 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000161 AC: 4AN: 247682Hom.: 0 AF XY: 0.0000149 AC XY: 2AN XY: 133792
GnomAD4 exome AF: 0.00000414 AC: 6AN: 1449360Hom.: 0 Cov.: 32 AF XY: 0.00000418 AC XY: 3AN XY: 718378
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 06, 2023 | The c.2502A>T (p.E834D) alteration is located in exon 17 (coding exon 17) of the NRP1 gene. This alteration results from a A to T substitution at nucleotide position 2502, causing the glutamic acid (E) at amino acid position 834 to be replaced by an aspartic acid (D). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at